miga-base 0.4.3.0 → 0.5.0.0

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.__mower.Rd

@@ -1,18 +1,17 @@
-\name{enve.recplot2.findPeaks.__mower}
-\alias{enve.recplot2.findPeaks.__mower}
-\title{enve recplot2 findPeaks   mower}
-\description{Internal ancilliary function (see `enve.recplot2.findPeaks.mower`).}
-\usage{enve.recplot2.findPeaks.__mower(peaks.opts)}
-\arguments{
-  \item{peaks.opts}{
-}
-}
-
-
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.__mower}
+\alias{enve.recplot2.findPeaks.__mower}
+\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder - Internal Ancillary Function 2}
+\usage{
+enve.recplot2.findPeaks.__mower(peaks.opts)
+}
+\arguments{
+\item{peaks.opts}{List of options for \code{\link{enve.recplot2.findPeaks.__mow_one}}}
+}
+\description{
+Internal ancillary function (see \code{\link{enve.recplot2.findPeaks.mower}}).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.em.Rd

@@ -1,33 +1,43 @@
-\name{enve.recplot2.findPeaks.em}
-\alias{enve.recplot2.findPeaks.em}
-\title{enve recplot2 findPeaks em}
-\description{Identifies peaks in the population histogram using a Gaussian Mixture
-Model Expectation Maximization (GMM-EM) method.}
-\usage{enve.recplot2.findPeaks.em(x, max.iter = 1000, ll.diff.res = 1e-08, 
-    components = 2, rm.top = 0.05, verbose = FALSE, init, log = TRUE)}
-\arguments{
-  \item{x}{An `enve.RecPlot2` object.}
-  \item{max.iter}{Maximum number of EM iterations.}
-  \item{ll.diff.res}{Maximum Log-Likelihood difference to be considered as convergent.}
-  \item{components}{Number of distributions assumed in the mixture.}
-  \item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
-This step is useful to remove highly conserved regions, but can be
-turned off by setting rm.top=0. The quantile is determined *after*
-removing zero-coverage windows.}
-  \item{verbose}{Display (mostly debugging) information.}
-  \item{init}{Initialization parameters. By default, these are derived from k-means
-clustering. A named list with vectors for 'mu', 'sd', and 'alpha', each
-of length `components`.}
-  \item{log}{Logical value indicating if the estimations should be performed in
-natural logarithm units. Do not change unless you know what you're
-doing.}
-}
-
-\value{Returns a list of `enve.RecPlot2.Peak` objects.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.em}
+\alias{enve.recplot2.findPeaks.em}
+\title{Enveomics: Recruitment Plot (2) Em Peak Finder}
+\usage{
+enve.recplot2.findPeaks.em(x, max.iter = 1000, ll.diff.res = 1e-08,
+  components = 2, rm.top = 0.05, verbose = FALSE, init, log = TRUE)
+}
+\arguments{
+\item{x}{An \code{\link{enve.RecPlot2}} object.}
+
+\item{max.iter}{Maximum number of EM iterations.}
+
+\item{ll.diff.res}{Maximum Log-Likelihood difference to be considered as convergent.}
+
+\item{components}{Number of distributions assumed in the mixture.}
+
+\item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
+This step is useful to remove highly conserved regions, but can be
+turned off by setting \code{rm.top=0}. The quantile is determined
+\strong{after} removing zero-coverage windows.}
+
+\item{verbose}{Display (mostly debugging) information.}
+
+\item{init}{Initialization parameters. By default, these are derived from k-means
+clustering. A named list with vectors for \code{mu}, \code{sd}, and
+\code{alpha}, each of length \code{components}.}
+
+\item{log}{Logical value indicating if the estimations should be performed in
+natural logarithm units. Do not change unless you know what you're
+doing.}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
+}
+\description{
+Identifies peaks in the population histogram using a Gaussian Mixture
+Model Expectation Maximization (GMM-EM) method.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.emauto.Rd

@@ -1,28 +1,36 @@
-\name{enve.recplot2.findPeaks.emauto}
-\alias{enve.recplot2.findPeaks.emauto}
-\title{enve recplot2 findPeaks emauto}
-\description{Identifies peaks in the population histogram using a Gaussian Mixture
-Model Expectation Maximization (GMM-EM) method with number of components
-automatically detected.}
-\usage{enve.recplot2.findPeaks.emauto(x, components = seq(1, 10), criterion = "aic", 
-    merge.tol = 2L, verbose = FALSE, ...)}
-\arguments{
-  \item{x}{An `enve.RecPlot2` object.}
-  \item{components}{A vector of number of components to evaluate.}
-  \item{criterion}{Criterion to use for components selection. Must be one of:
-'aic' (Akaike Information Criterion),
-'bic' or 'sbc' (Bayesian Information Criterion or Schwarz Criterion).}
-  \item{merge.tol}{When attempting to merge peaks with very similar sequencing depth, use
-this number of significant digits (in log-scale).}
-  \item{verbose}{Display (mostly debugging) information.}
-  \item{\dots}{Any additional parameters supported by `enve.recplot2.findPeaks.em`.}
-}
-
-\value{Returns a list of `enve.RecPlot2.Peak` objects.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.emauto}
+\alias{enve.recplot2.findPeaks.emauto}
+\title{Enveomics: Recruitment Plot (2) Emauto Peak Finder}
+\usage{
+enve.recplot2.findPeaks.emauto(x, components = seq(1, 10),
+  criterion = "aic", merge.tol = 2L, verbose = FALSE, ...)
+}
+\arguments{
+\item{x}{An \code{\link{enve.RecPlot2}} object.}
+
+\item{components}{A vector of number of components to evaluate.}
+
+\item{criterion}{Criterion to use for components selection. Must be one of:
+\code{aic} (Akaike Information Criterion),
+\code{bic} or \code{sbc} (Bayesian Information Criterion or Schwarz Criterion).}
+
+\item{merge.tol}{When attempting to merge peaks with very similar sequencing depth, use
+this number of significant digits (in log-scale).}
+
+\item{verbose}{Display (mostly debugging) information.}
+
+\item{...}{Any additional parameters supported by \code{\link{enve.recplot2.findPeaks.em}}.}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
+}
+\description{
+Identifies peaks in the population histogram using a Gaussian Mixture
+Model Expectation Maximization (GMM-EM) method with number of components
+automatically detected.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.findPeaks.mower.Rd

@@ -1,56 +1,74 @@
-\name{enve.recplot2.findPeaks.mower}
-\alias{enve.recplot2.findPeaks.mower}
-\title{enve recplot2 findPeaks mower}
-\description{Identifies peaks in the population histogram potentially indicating
-sub-population mixtures, using a custom distribution-mowing method.}
-\usage{enve.recplot2.findPeaks.mower(x, min.points = 10, quant.est = c(0.002, 
-    0.998), mlv.opts = list(method = "parzen"), fitdist.opts.sn = list(distr = "sn", 
-    method = "qme", probs = c(0.1, 0.5, 0.8), start = list(omega = 1, 
-        alpha = -1), lower = c(0, -Inf, -Inf)), fitdist.opts.norm = list(distr = "norm", 
-    method = "qme", probs = c(0.4, 0.6), start = list(sd = 1), 
-    lower = c(0, -Inf)), rm.top = 0.05, with.skewness = TRUE, 
-    optim.rounds = 200, optim.epsilon = 1e-04, merge.logdist = log(1.75), 
-    verbose = FALSE, log = TRUE)}
-\arguments{
-  \item{x}{An `enve.RecPlot2` object.}
-  \item{min.points}{Minimum number of points in the quantile-estimation-range
-(`quant.est`) to estimate a peak.}
-  \item{quant.est}{Range of quantiles to be used in the estimation of a peak's
-parameters.}
-  \item{mlv.opts}{Ignored. For backwards compatibility.}
-  \item{fitdist.opts.sn}{
-}
-  \item{fitdist.opts.norm}{
-}
-  \item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
-This step is useful to remove highly conserved regions, but can be
-turned off by setting rm.top=0. The quantile is determined *after*
-removing zero-coverage windows.}
-  \item{with.skewness}{Allow skewness correction of the peaks. Typically, the
-sequencing-depth distribution for a single peak is left-skewed, due
-partly (but not exclusively) to fragmentation and mapping sensitivity.
-See Lindner et al 2013, Bioinformatics 29(10):1260-7 for an
-alternative solution for the first problem (fragmentation) called
-"tail distribution".}
-  \item{optim.rounds}{Maximum rounds of peak optimization.}
-  \item{optim.epsilon}{Trace change at which optimization stops (unless `optim.rounds` is
-reached first). The trace change is estimated as the sum of square
-differences between parameters in one round and those from two rounds
-earlier (to avoid infinite loops from approximation).}
-  \item{merge.logdist}{Maximum value of |log-ratio| between centrality parameters in peaks to
-attempt merging. The default of ~0.22 corresponds to a maximum
-difference of 25\%.}
-  \item{verbose}{Display (mostly debugging) information.}
-  \item{log}{Logical value indicating if the estimations should be performed in
-natural logarithm units. Do not change unless you know what you're
-doing.}
-}
-
-\value{Returns a list of `enve.RecPlot2.Peak` objects.}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.findPeaks.mower}
+\alias{enve.recplot2.findPeaks.mower}
+\title{Enveomics: Recruitment Plot (2) Mowing Peak Finder}
+\usage{
+enve.recplot2.findPeaks.mower(x, min.points = 10, quant.est = c(0.002,
+  0.998), mlv.opts = list(method = "parzen"),
+  fitdist.opts.sn = list(distr = "sn", method = "qme", probs = c(0.1,
+  0.5, 0.8), start = list(omega = 1, alpha = -1), lower = c(0, -Inf,
+  -Inf)), fitdist.opts.norm = list(distr = "norm", method = "qme", probs
+  = c(0.4, 0.6), start = list(sd = 1), lower = c(0, -Inf)),
+  rm.top = 0.05, with.skewness = TRUE, optim.rounds = 200,
+  optim.epsilon = 1e-04, merge.logdist = log(1.75), verbose = FALSE,
+  log = TRUE)
+}
+\arguments{
+\item{x}{An \code{\link{enve.RecPlot2}} object.}
+
+\item{min.points}{Minimum number of points in the quantile-estimation-range
+\code{(quant.est)} to estimate a peak.}
+
+\item{quant.est}{Range of quantiles to be used in the estimation of a peak's
+parameters.}
+
+\item{mlv.opts}{Ignored. For backwards compatibility.}
+
+\item{fitdist.opts.sn}{Options passed to \code{fitdist} to estimate the standard deviation if
+\code{with.skewness=TRUE}. Note that the \code{start} parameter will be
+ammended with \code{xi=estimated} mode for each peak.}
+
+\item{fitdist.opts.norm}{Options passed to \code{fitdist} to estimate the standard deviation if
+\code{with.skewness=FALSE}. Note that the \code{start} parameter will be
+ammended with \code{mean=estimated} mode for each peak.}
+
+\item{rm.top}{Top-values to remove before finding peaks, as a quantile probability.
+This step is useful to remove highly conserved regions, but can be
+turned off by setting \code{rm.top=0}. The quantile is determined
+\strong{after} removing zero-coverage windows.}
+
+\item{with.skewness}{Allow skewness correction of the peaks. Typically, the
+sequencing-depth distribution for a single peak is left-skewed, due
+partly (but not exclusively) to fragmentation and mapping sensitivity.
+See \emph{Lindner et al 2013, Bioinformatics 29(10):1260-7} for an
+alternative solution for the first problem (fragmentation) called
+"tail distribution".}
+
+\item{optim.rounds}{Maximum rounds of peak optimization.}
+
+\item{optim.epsilon}{Trace change at which optimization stops (unless \code{optim.rounds} is
+reached first). The trace change is estimated as the sum of square
+differences between parameters in one round and those from two rounds
+earlier (to avoid infinite loops from approximation).}
+
+\item{merge.logdist}{Maximum value of \code{|log-ratio|} between centrality parameters in peaks
+to attempt merging. The default of ~0.22 corresponds to a maximum
+difference of 25\%.}
+
+\item{verbose}{Display (mostly debugging) information.}
+
+\item{log}{Logical value indicating if the estimations should be performed in
+natural logarithm units. Do not change unless you know what you're
+doing.}
+}
+\value{
+Returns a list of \code{\link{enve.RecPlot2.Peak}} objects.
+}
+\description{
+Identifies peaks in the population histogram potentially indicating
+sub-population mixtures, using a custom distribution-mowing method.
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.peak-class.Rd

@@ -1,46 +1,59 @@
-\name{enve.RecPlot2.Peak-class}
-\Rdversion{1.1}
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
 \docType{class}
+\name{enve.RecPlot2.Peak-class}
 \alias{enve.RecPlot2.Peak-class}
 \alias{enve.RecPlot2.Peak}
-%% \alias{$}
-
-\title{enve.RecPlot2.Peak S4 class}
-\description{Enve-omics representation of a peak in the sequencing depth histogram
-of a Recruitment plot (see `enve.recplot2.findPeaks`).}
-\section{Objects from the Class}{Objects can be created by calls of the form \code{new(enve.RecPlot2.Peak ...)}}
+\title{Enveomics: Recruitment Plot (2) Peak - S4 Class}
+\description{
+Enve-omics representation of a peak in the sequencing depth histogram
+of a Recruitment plot (see \code{\link{enve.recplot2.findPeaks}}).
+}
 \section{Slots}{
-  \describe{
-    \item{\code{dist}:}{(\code{character}) Distribution of the peak. Currently supported: 'norm' (normal) and 'sn'
+
+\describe{
+\item{\code{dist}}{\code{(character)}
+Distribution of the peak. Currently supported: \code{norm} (normal) and \code{sn}
 (skew-normal).}
-    \item{\code{values}:}{(\code{numeric}) Sequencing depth values predicted to conform the peak.}
-    \item{\code{values.res}:}{(\code{numeric}) Sequencing depth values not explained by this or previously identified
+
+\item{\code{values}}{\code{(numeric)}
+Sequencing depth values predicted to conform the peak.}
+
+\item{\code{values.res}}{\code{(numeric)}
+Sequencing depth values not explained by this or previously identified
 peaks.}
-    \item{\code{mode}:}{(\code{numeric}) Seed-value of mode anchoring the peak.}
-    \item{\code{param.hat}:}{(\code{list}) Parameters of the distribution. A list of two values if dist='norm' (sd
-and mean), or three values if dist='sn' (omega=scale, alpha=shape, and
+
+\item{\code{mode}}{\code{(numeric)}
+Seed-value of mode anchoring the peak.}
+
+\item{\code{param.hat}}{\code{(list)}
+Parameters of the distribution. A list of two values if dist=\code{norm} (sd
+and mean), or three values if dist=\code{sn}(omega=scale, alpha=shape, and
 xi=location). Note that the "dispersion" parameter is always first and
 the "location" parameter is always last.}
-    \item{\code{n.hat}:}{(\code{numeric}) Number of bins estimated to be explained by this peak. This should
-ideally be equal to the length of `values`, but it's not and integer.}
-    \item{\code{n.total}:}{(\code{numeric}) Total number of bins from which the peak was extracted. I.e., total
+
+\item{\code{n.hat}}{\code{(numeric)}
+Number of bins estimated to be explained by this peak. This should
+ideally be equal to the length of  \code{values}, but it's not an integer.}
+
+\item{\code{n.total}}{\code{(numeric)}
+Total number of bins from which the peak was extracted. I.e., total
 number of position bins with non-zero sequencing depth in the recruitment
 plot (regardless of peak count).}
-    \item{\code{err.res}:}{(\code{numeric}) Error left after adding the peak (mower) or log-likelihood (em or emauto).}
-    \item{\code{merge.logdist}:}{(\code{numeric}) Attempted `merge.logdist` parameter.}
-    \item{\code{seq.depth}:}{(\code{numeric}) Best estimate available for the sequencing depth of the peak (centrality).}
-    \item{\code{log}:}{(\code{logical}) Indicates if the estimation was performed in natural logarithm space}
-  }
-}
-\section{Methods}{
-  \describe{
-    \item{$}{\code{signature(x = "enve.RecPlot2.Peak")}: ... }
-	 }
-}
-
-\author{Luis M. Rodriguez-R [aut, cre]}
 
+\item{\code{err.res}}{\code{(numeric)}
+Error left after adding the peak (mower) or log-likelihood (em or emauto).}
 
+\item{\code{merge.logdist}}{\code{(numeric)}
+Attempted \code{merge.logdist} parameter.}
 
+\item{\code{seq.depth}}{\code{(numeric)}
+Best estimate available for the sequencing depth of the peak (centrality).}
 
+\item{\code{log}}{\code{(logical)}
+Indicates if the estimation was performed in natural logarithm space.}
+}}
 
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}

data/utils/enveomics/enveomics.R/man/enve.recplot2.seqdepth.Rd

@@ -1,22 +1,27 @@
-\name{enve.recplot2.seqdepth}
-\alias{enve.recplot2.seqdepth}
-\title{enve recplot2 seqdepth}
-\description{Calculate the sequencing depth of the given window(s)}
-\usage{enve.recplot2.seqdepth(x, sel, low.identity = FALSE)}
-\arguments{
-  \item{x}{`enve.RecPlot2` object.}
-  \item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
-passed, it returns the sequencing depth of all windows}
-  \item{low.identity}{A logical indicating if the sequencing depth is to be estimated only
-with low-identity matches. By default, only high-identity matches are
-used.}
-}
-
-\value{Returns a numeric vector of sequencing depths (in bp/bp). }
-
-\author{Luis M. Rodriguez-R [aut, cre]}
-
-
-
-
-
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/recplot2.R
+\name{enve.recplot2.seqdepth}
+\alias{enve.recplot2.seqdepth}
+\title{Enveomics: Recruitment Plot (2) Sequencing Depth}
+\usage{
+enve.recplot2.seqdepth(x, sel, low.identity = FALSE)
+}
+\arguments{
+\item{x}{\code{\link{enve.RecPlot2}} object.}
+
+\item{sel}{Window(s) for which the sequencing depth is to be calculated. If not
+passed, it returns the sequencing depth of all windows.}
+
+\item{low.identity}{A logical indicating if the sequencing depth is to be estimated only
+with low-identity matches. By default, only high-identity matches are
+used.}
+}
+\value{
+Returns a numeric vector of sequencing depths (in bp/bp).
+}
+\description{
+Calculate the sequencing depth of the given window(s).
+}
+\author{
+Luis M. Rodriguez-R [aut, cre]
+}